I have a shot that i have slowed to 15% and looks and plays perfectly in the canvas with frame blending on.
When I render the video the output is glitchy, looks as though frame blending has been turned off.

It hasn't been turned off though. I have checked the box "Frame Blending for Speed" in the render control dialog. I also rendered the video with this setting off and the render was even more glitchy, so it obviously does something but is it the same frame blending algorithm that is use for the preview in canvas?

Any help with this would be greatly appreciated, it may not even be a frame blending problem,